Recombination analysis of full-length genome of PRRSV strains isolated in China 2013-2015

Porcine reproductive and respiratory syndrome (PRRS), caused by PRRS virus (PRRSV), still engenders immense economic losses to the swine industry worldwide. The co-existence of multi–type stains, rapid evolutionary rate and possible recombination of PRRSV lead to increased genetic diversity. Here we report the important recombination of 3 Chinese PRRSV strains collected during 2013-2015.

Full-length genome of four PRRSV isolates from swine herds in central China from 2013 to 2015 named as HENAN-XINX,HENANHEB,HENZMD-9 and HENZK-1, respectively, were obtained by RT-PCR and analyzed together with 24 reference strains including serotypes 1(EU) and 2(NA) strains by ClustalW and RDP3.44 softwares to retrieve possible recombination event. The authenticity of the event was verified by sequence analyzing of each part of the recombination.

Compared with references, three (HENAN-XINX, HENAN-HEB and HENZMD9) of 4 isolates were identified as genome recombination strains. All recombination events occurred among NA not EU serotype strains. Acting as a backbone of all 3 variants isolated in this study, strain NADC30 recombined with NSP2-5 genes（4188-5997 nt） of a classical PRRSV strain S1 resulted in HENAN-XINX, recombined with NSP2 gene (1352-2135 nt) of a HPPRRSV strain 09JS resulted in HENAN-HEB , whereas recombined with the genes of 2 HP-PRRSV strains, 5’ UTR and NSP1-2 genes (1-1499 nt) of strain GX1002 and NSP2-9 genes (4093-7640 nt) of strain JXA1-P45, resulted in HENZMD9. However, there was no evidence of recombination in HP-PRRSV strain HENZK-1.

As a common pattern of genetic variation for RNA viruses, recombination is important to virus evolutionary process. PRRSV recombination was firstly reported in 1997. Since 1996, all classic, HP- and NADC30-like PRRSV strains belonging to NA serotype have been reported in China successively, and recently EU serotype strain was also reported. Thus, PRRSV strains developed diversified, and the co-existence of different strains in a pig farm enhances the risk of PRRSV recombination, which is one of the important factors making the PRRS control difficult. This study indicated that a) all three kinds of NA serotype PRRSV(classical, HP- and NADC30-like) co-existed in the herds in China. b) Three isolates were identified as variants derived from the recombination between Chinese strains (S1, 09JS , GX1002 and JXA1-P45)and USA strain NADC30 and c)As a backbone virus strain NADC30 suggested a strong ability to receive the foreign genes from the other NA serotype PRRSVs, but the mechanism remains unknown.The study on the pathogenicity of the isolates is under conduction.

Disclosure of Interest: None Declared.